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Differential expression gene analysis: how to do t.test on expression matrix with goups different clinical matrix?
How to make a great R reproducible exampleT test to find differentially expressed genes in Rdifferentially expressed genes in RUsing SVM for gene expression analysisCreating eset object from preprocessed expression matrix?Differential gene expression analysis in PythonHierarchical clustering on continuous heterogeneous variables with different range/scales in RHow to do Gene Expression dataset analysis with RUsing limma for Differential Expression with log2 Normalized RT-qPCR dataExtracting genes differentially expressed by Wilcox test
.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty margin-bottom:0;
I am beginning my PhD in transcriptome (affymetrix assay) analysis.
I have an expression matrix (trans_data : 32000 genes x 620 samples), and a clinical matrix (clin_data : 620 samples x 42 clinical caracteristics).
The samples belong to 1 of the 4 populations A-B-C-D. I'd like to draw comparision of gene expression between population A and B without triying to bind the two matrix.
I'd like to optain a matrix with mean expression of each genes in the two population, then pvalue, then adjusted p value.
Then I could select only differentially expressed genes (padj < 0,05).
thanks for your help.
Alain
r
asked Mar 28 at 16:53
Alain_LUAlain_LU
111 bronze badge
add a comment
|
I am beginning my PhD in transcriptome (affymetrix assay) analysis.
I have an expression matrix (trans_data : 32000 genes x 620 samples), and a clinical matrix (clin_data : 620 samples x 42 clinical caracteristics).
The samples belong to 1 of the 4 populations A-B-C-D. I'd like to draw comparision of gene expression between population A and B without triying to bind the two matrix.
I'd like to optain a matrix with mean expression of each genes in the two population, then pvalue, then adjusted p value.
Then I could select only differentially expressed genes (padj < 0,05).
thanks for your help.
Alain
r
asked Mar 28 at 16:53
Alain_LUAlain_LU
111 bronze badge
add a comment
|
I am beginning my PhD in transcriptome (affymetrix assay) analysis.
I have an expression matrix (trans_data : 32000 genes x 620 samples), and a clinical matrix (clin_data : 620 samples x 42 clinical caracteristics).
The samples belong to 1 of the 4 populations A-B-C-D. I'd like to draw comparision of gene expression between population A and B without triying to bind the two matrix.
I'd like to optain a matrix with mean expression of each genes in the two population, then pvalue, then adjusted p value.
Then I could select only differentially expressed genes (padj < 0,05).
thanks for your help.
Alain
r
asked Mar 28 at 16:53
Alain_LUAlain_LU
111 bronze badge
I am beginning my PhD in transcriptome (affymetrix assay) analysis.
I have an expression matrix (trans_data : 32000 genes x 620 samples), and a clinical matrix (clin_data : 620 samples x 42 clinical caracteristics).
The samples belong to 1 of the 4 populations A-B-C-D. I'd like to draw comparision of gene expression between population A and B without triying to bind the two matrix.
I'd like to optain a matrix with mean expression of each genes in the two population, then pvalue, then adjusted p value.
Then I could select only differentially expressed genes (padj < 0,05).
thanks for your help.
Alain
r
r
asked Mar 28 at 16:53
Alain_LUAlain_LU
111 bronze badge
asked Mar 28 at 16:53
Alain_LUAlain_LU
111 bronze badge
asked Mar 28 at 16:53
Alain_LUAlain_LU
111 bronze badge
asked Mar 28 at 16:53
Alain_LUAlain_LU
111 bronze badge
asked Mar 28 at 16:53
Alain_LUAlain_LU
111 bronze badge
111 bronze badge
add a comment
|
add a comment
|
1 Answer
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Can't answer your question directly without a clear reproducible example but you might want to check out the rather excellent tableone package
answered Mar 28 at 17:13
B_RealB_Real
528 bronze badges
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Can't answer your question directly without a clear reproducible example but you might want to check out the rather excellent tableone package
answered Mar 28 at 17:13
B_RealB_Real
528 bronze badges
add a comment
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Can't answer your question directly without a clear reproducible example but you might want to check out the rather excellent tableone package
answered Mar 28 at 17:13
B_RealB_Real
528 bronze badges
add a comment
|
Can't answer your question directly without a clear reproducible example but you might want to check out the rather excellent tableone package
answered Mar 28 at 17:13
B_RealB_Real
528 bronze badges
Can't answer your question directly without a clear reproducible example but you might want to check out the rather excellent tableone package
answered Mar 28 at 17:13
B_RealB_Real
528 bronze badges
answered Mar 28 at 17:13
B_RealB_Real
528 bronze badges
answered Mar 28 at 17:13
B_RealB_Real
528 bronze badges
answered Mar 28 at 17:13
B_RealB_Real
528 bronze badges
528 bronze badges
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